bio-epitranscriptomics-m6a-peak-calling
Call m6A peaks from MeRIP-seq IP vs input comparisons. Use when identifying m6A modification sites from methylated RNA immunoprecipitation data.
npx skills add majiayu000/claude-skill-registry --skill m6a-peak-calling-gptomics-bioskills --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
# m6A Peak Calling ## exomePeak2 (Recommended) ```r library(exomePeak2) # Peak calling with biological replicates result <- exomePeak2( bam_ip = c('IP_rep1.bam', 'IP_rep2.bam'), bam_input = c('Input_rep1.bam', 'Input_rep2.bam'), gff = 'genes.gtf', genome = 'hg38', paired_end = TRUE ) # Export peaks exportResults(result, format = 'BED') ``` ## MACS3 Alternative ```bash # Call peaks treating input as control macs3 callpeak \ -t IP_rep1.bam IP_rep2.bam \ -c Input_rep1.bam Input_rep2.bam \ -f BAMPE \ -g hs \ -n m6a_peaks \ --nomodel \ --extsize 150 \ -q 0.05 ``` ## MeTPeak ```r library(MeTPeak) # GTF-aware peak calling metpeak( IP_BAM = c('IP_rep1.bam', 'IP_rep2.bam'), INPUT_BAM = c('Input_rep1.bam', 'Input_rep2.bam'), GENE_ANNO_GTF = 'genes.gtf', OUTPUT_DIR = 'metpeak_output' ) ``` ## Peak Filtering ```bash # Filter by fold enrichment and q-value # FC > 2, q < 0.05 typical thresholds awk '$7 > 2 && $9 < 0.05' peaks.xls > filtered_peaks.bed ``` ## Related Skills - merip-preprocessing - Prepare data for peak calling - m6a-differential - Compare peaks between conditions - chip-seq/peak-calling - Similar concepts
- exomePeak2 (Recommended)
- MACS3 Alternative
- MeTPeak
- Peak Filtering
- Related Skills
Call peaks treating input as control macs3 callpeak \ Filter by fold enrichment and q-value FC > 2, q < 0.05 typical thresholds awk '$7 > 2 && $9 < 0.05' peaks.xls > filtered_peaks.bed
What does the bio-epitranscriptomics-m6a-peak-calling skill do?
Call m6A peaks from MeRIP-seq IP vs input comparisons. Use when identifying m6A modification sites from methylated RNA immunoprecipitation data.
How do I install it?
Run `npx skills add majiayu000/claude-skill-registry --skill m6a-peak-calling-gptomics-bioskills --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From majiayu000/claude-skill-registry, a repository with 534 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.